SOAPdenovo statistics output for Nx

Question

[deepti1rao]

Here's the Nx output that I have got on running SOAPdenovo. Does column 2 represent L50 and column 3 N50?? Please clarify.

N10 2252 11403 N20 1611 29595 N30 1239 53911 N40 982 84988 N50 781 124052 N60 621 173134 N70 489 235218 N80 382 314436 N90 196 433979

General statistics are as follows:

Contig_Num 694440 Mean_Size 491 Median_Size 350 Longest_Seq 30470 Shortest_Seq 116

[lakhujanivijay]

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Answer 1

[Tm]

SOAPdenovo statistics file represents 3 column namely:

• 1st column represents : N10, N20, N30, N40, N50 .....N90
• 2nd column represents : Respective values of N10 ....N90
• 3rd column represents : Respective values of L10...L90 i.e Number of scaffolds whose length sum help fulfilling the 2nd column values

For instance, in your case:

• N10 value is 2252 and 11403 are the smallest number of contigs/scaffolds whose length sum N10 value and thus it represents L10
• N50 value is 781 and 124052 are the smallest number of contigs/scaffolds whose length sum N50 value and thus it represents L50

So, it is opposite of what you are thinking.